The full story
With S.H.I.E.L.D. gutted and Hydra still active, Coulson rebuilds the agency from a hidden base, recruiting an expanded team while keeping its existence a secret even from most of its own agents. His resurrection side effect worsens: he's driven to carve the alien symbol from last season onto every surface he can find, until the team realizes the carvings form a three-dimensional map, and the compulsion finally stops once he understands what it points to.
Grant Ward, held prisoner, remains a wild card rather than a simple villain -- he offers information in exchange for freedom, escapes, and starts working his own angle against both S.H.I.E.L.D. and his old Hydra allies, brainwashing former agent Kara "Agent 33" Palamas into an ally along the way. Elsewhere, a faction led by Agent Bobbi Morse breaks off as "Real S.H.I.E.L.D.," distrusting Coulson's secrecy and his growing reliance on unproven, potentially dangerous recruits -- a rift that's resolved only when the two sides merge back together under Coulson's command.
The map leads to a hidden Kree city built around Terrigen crystals capable of transforming certain humans -- Inhumans -- into people with genuine superhuman abilities. Skye is one of them: her real name is Daisy Johnson, and the map was built by her own father, Calvin "Cal" Johnson, a brilliant, unstable scientist who has spent years searching for the daughter he lost. Skye's mother, Jiaying, leads a hidden Inhuman sanctuary called Afterlife, and at first offers Skye the family and belonging she's never had.
Hydra's last major leader, Daniel Whitehall, turns out to be a Nazi scientist named Werner Reinhardt who has kept himself alive for decades using an Inhuman's regenerative blood, and who is hunting an ancient artifact called the Diviner to unlock more Inhuman potential. Coulson feeds the Avengers a tip on Whitehall's location, sending them to the Hydra base whose fall opens Avengers: Age of Ultron. Jemma Simmons, investigating the same Diviner, is pulled into it and vanishes into an unknown void just as the season heads into its finale.
Jiaying, it turns out, has been manipulating both her daughter and her people, sustaining her own long life by draining the life force of others, and she engineers a war with S.H.I.E.L.D. to protect Afterlife's secrecy. In the finale, Coulson loses an arm stopping a Terrigen crystal detonation, and Daisy is forced to fight her own mother, who nearly kills her in turn before Cal -- finally seeing what Jiaying really is -- kills her himself. The season ends with Daisy staying on with S.H.I.E.L.D. as a full agent, Cal's memory wiped clean, Ward rebuilding what's left of Hydra on his own terms, and Fitz and Simmons's reunion cut short: Simmons is still missing, swallowed by the ancient artifact -- now revealed to be a portal called the Monolith.